City of Dust
by the.empress
Summary: With the battle over, and Valentine dead, Jace becomes confused about his identity and leaves Clary to fight a battle of his own. But as Sebastion comes lurking, there is danger for all the people Clary loves, but this she must fight on her own.
1. Unwanted returns

The night grew darker as a young girl sat on the side the road. Her glowing red hair became increasingly noticeable as taxi's circulated the streets of down town Brooklyn. Years ago she would have been afraid, but now the longing she felt to see the boy she had loved took over her better judgment. In her hands she held the small ring with her families emblem engraved. It meant nothing to her. She knew her father for what he was, she could never be proud to be his daughter.

A shadow darted across the now empty street. Startled she reached into her pocket and pulled out a small silver steel which looked almost translucent as the light from the flickering street lights bounced of it. Holding onto the steel tight, she did not proceed to stand, but just sat watching the road as the footsteps grew closer.

"Clary," said a familiar voice with disgust. It seemed more like it was being spat at her then saying her name. "You are not the person I wished to meet here tonight."

Clary sighed and proceeded to stand up to stare her brother straight in the eyes. "Neither are you, I must say. What is it that you want?" her tone was threatening, but more so was the steel she held between the two. To many this was none of a weapon, but Clary was able to do magnificent things, to cause pain to anyone. Knowing this he took a step back.

"I am here strictly to see your _boyfriend _Jace, sister. We have some unfinished matters to attend to, but does he know that you have chosen to face me alone tonight"

She thought about the question for longer then she should have. No Jace did not know she was here. But it wasn't as if she had had the chance to tell him. He had left about a month ago, on a quest to find out who he was, after discovering that all who he thought were family were not, on a few occasions. He had become depressed and was making everyone suffer too.  
"I can take care of myself," she replied with the same hit of disgust and anger Sebastian had used.

"I do not doubt that young Clary, but as your brother I do not think it is wise for you to hang around the streets by yourself. There are worse things lurking in the dark then me." With the slightest sound of sympathy he turned on his heal and walk away.

"Wait!" Clary couldn't believe she had just said that. It seemed to just slip through her, but she had so many questions. Seb may be her brother, but mean nothing in that sense, but he held the secrets about her fathers past and her future.

"That would not be wise. Creatures are beginning to lurk, talking about the life that Valentine had created for them by being his aly. I am not the only one who will be avenging my father's death. Whilst I will not harm you or our mother, the circle is at fault for the death of their leader, and they will be accounted for."

With that he disappeared without giving Clary time to respond. What did he mean? Her mother was apart of the circle, but why did Sebastian have her well being at heart? After all previously he would have been the one to harm either of them. They weren't the only members in New York though and it was only now that Clary understood why he was truly here.

***

It had been days since Jace had seen any existence from the world he lived in. The demon free lifestyle of the country was relaxing as he journeyed across the land. The more he thought about it, the less it all made sense. Up until a few months ago he was sure of whom he was. He was Jonathan Wayland. Now he was just Jace. He was a Lightwood by heart, but by truth he didn't know what he was.  
He envied Clary in this way. Her perspectives of people didn't change, even when she found out that the man she feared was her father. But he was still a monster to her. That same man had raised Jace, and it made him question whether he was more evil than good. And he knew that he could never be happy till he was assured that all the evil his mentor had passed on to him had disappeared.

He wasn't alone on his journey. Clary had sent her best friend Simon to follow closely behind, but keeping enough distance so that he wasn't aware of his follower. But he knew. Instead of lashing out at Simon though, he counted it as a positive, that it anything went wrong, someone would be able to explain to Clary or the lightwoods what had happened. Simon was with his girlfriend Mia. They were the complete opposites, but when fighting together the posed powers greater than any other. It was her distinctive howling in the night that gained Jace the knowledge they were there.

Leaving Clary in New York was the hardest thing he had had to do. She would have fought a war to come with him and as much as he wanted her to, she had to refuse. He did not take his journey too lightly. He may not have a purpose, but he had a destination and that was Change

***

Clary began to race through the streets of Brooklyn and a pace she never believed possible. The church was too far away, she didn't have time enough to make it there and tell the others. It was Luke who she needed now. He was in danger too, but he was also the best when it came to defending himself. The bookshop was locked up for the night, so she had to sneak through the back door, with the key Luke had hidden for her last year as he knew how often it was that she forgot her key.

She had still been living with Luke since her mother had been awake. Her mother had found a small apartment which she used as her art studio, and had proceeded to explain that why her and Luke worked out their differences, she preferred that Clary was safe with him, under the protection of the wolfs.

The house had an eerie smell and the floors seemed to be flooded with a thick black mass that covered that was much denser then water. Clary pulled the witch light out of her pocked and shined it around the room. What she saw shook her and stopped her in her place. In thick red blood the words _I'll get you _shone from every inch of the wall. It was now that Clary feared for the life of Lucian Graymark. With her steel in one hand, and the ring of her father in the other she ran through the dark streets in search of the help she needed to protect her family.


	2. forgetting not

*a month before*

They sat in the small living room of the house behind the bookstore. Silence circled the room and neither could think of what next to say. Jace's blond hair was ruffled and had a dirty tinge to it, Clary's was silk and sleek, the vibrant red flowing around her face making her look more and more beautiful. The night crept on around them as the silence grew unbearable, and just to break the suspense Clary coughed a fake, yet noticeably fake cough.

"I don't like you hanging out at that club," Jace's words were strong and harsh. However he kept a bemused look on his face, confusing Clary as she could no longer tell if he was serious. She was annoyed though. He couldn't control where she went when she wasn't with him, and it wasn't like having a vampire follow you round meant that your life was constantly at risk. Simon would always protect her.

"why?" were the only words she could bring herself to say. But she knew the answer. It was because it was her and Simon's thing; together they would go to pandemonium and dance till the night was old before finding their way home to bed before sunrise. All these things, being something Clary wouldn't invite Jace to, did she think he was not fun enough? They had met in Pandemonium after all.

"It's dangerous." He didn't elaborate; he just looked down at the floor and began to examine his shoe laces. It wasn't for a few moments later that he looked up with a quirky expression on his face to realize that she wasn't sharing it. Tears ran down her narrow face without making a sound, and when she realized he was watching her she wiped them away.

Jace rose from his chair ad knelt before Clary, so that their faces were level. With his smooth fingers he wiped her tears off her cheeks before lifting her chin up to meet her eyes. There was sorrow hidden behind the bright blue eyes which usually made him grateful. he sighed.

"To you Clary Fray I owe my life and my love. One shadow hunters oath to another, in your eyes I will forever be lost, and in my heart you will forever be held. Forever and always"

He lent forward to lay his lips against hers, and for those moments, he began to forget the world. Nothing no longer mattered to him. He was hers. And she was his.

***

After what seemed like ages, Clary stopped herself from running. She was panting as she reached into her pocket and pulled out the witch light Jace had given her for her birthday.  
She couldn't remember a time when she had been so happy. For once she truly felt accepted, and not the accepted which Simon made her feel, but she felt _Loved.  
_Never when her and Simon were dating did she feel that way, the way she felt about Jace. But at the time he was her brother, it was wrong for them to be in love. He was meant to watch out for any guys chasing after her. Not be one of them.  
The whole thought of all this made her sick in the stomach. She never wanted to be defying nature, even though now she knew that they were not really related.  
She took a deep breath to clear her thoughts. She could worry about Jace later, now it was Luke that needed her help. With her steel in her hand she began to scribble a pattern of familiar lines through the wall of one of the buildings. What she drew slowly turned into a golden arched door, glowing bright with many colours swirling around, lighting up the footpath.

Looking around the street she searched to see if anyone else was around, before holding her breathing, and leaping through the arch. Her last thought being those of the church where the lightwoods lived.

***

Isabelle was the first person which Clary found when she entered the long hall of the institute where the lightwoods lived. She was walking around in her pajamas in search of something which Clary didn't understand. But it looked as if she had just came from Max's room, as in her hands, she had a small toy and a few anime books.  
It was then that Clary noticed she looked like she had been crying, but there was no time for that.

"ISSI I NEED YOUR HELP," Clary yelled down the hall. Isabelle was taken aback, startled as she quickly threw her stuff to the ground and wiped her face before staring blankly.  
"Its Sebastian, I mean Jonathan, I mean _my brother_, Valentines son, he is after Luke, and your parents, we need to stop him! And I don't know what to do." Her voice sounded needy as she pleaded.  
Isabelle was the last person she ever expected herself to be pleading for help. They had never gotten along well, due to the fact that Issi knew how Jace felt about Clary, and she still didn't think it was right. But Clary tried to put all their differences aside, numerous times. This was one of them circumstances.

"I spoke with him tonight. He wants to make them pay for the death of Valentine."

Blank stares crossed her face as she looked at Clary with a quirky expression.  
"Sebastian is dead. You were there when died. You told us all that," her voice was harsh as sending Clary into a state where she could not speak. It took her almost over a minute to regain her confidence.

"No one ever found proof! His body was never found; they said it may have washed down the river! Trust me!" Clary was no longer in the mood to keep trying to convince people. She just turned around and walked to elevator, trying to think of a plan herself, then it hit her.


	3. the scent of rise

Walking up to the abandoned city at night scared Clary. She had been here before but never without the company of Jace or the silent brothers, which she still couldn't consider if that was a good thing or not. She tried to make no noise, afraid that she would disturb the hundreds of shadow hunters which lay within the walls.

Thoughts of her mother and Luke ran through her head. She knew she had no choice and that she'd have to hurry. Sebastian was out there searching for Luke. How long could it be before he found him? As after all, he was Valentines son, part demon. His instincts wouldn't let him down.

The silence was eerie. Which was unusual for a silent city to be. But Clary could hear the screams of the silent brothers as they were tortured. Ringing through her mind as if it was really happening.  
She came to a halt at a stair case which went both up and down. Thinking hard she decided on her path. And with her witchlight guiding the way, she continued down the stairs towards the prison where Jace had been captivated.

The dungeons reeked of demon blood and what Clary thought might be rotting flesh. Holding her breath, she walked past all the cells without daring to glimpse inside. Shivers ran through her the as hall she had just walked ended with another plummeting stair case, leading her further and further underground.

A small room, smaller than the cell she remembered rescuing Jace from a year earlier grew suddenly as the stairs ended. The room was bare. All except for a large painting on the opposite wall. Using her hands, Clary felt along the wall to guide her around the room. Before coming to a stop in front of the painting.

Alicante's towers grew high in the hair, glowing slightly. With what would seem to any mundane as the most glorious fireworks, but Clary knew better. She waved her hard over the painting slowly as she concentrated hard on extracting whatever was hidden within. Within moments though, she began to sense she was not alone, as footsteps began to echo down the long stair case through the room she was standing in.

**

Thoughts of Clary wandered through Jake's head preventing him from sleeping at night. During the day he walked, leaving himself so exhausted that he hoped for once the pain would stop and he would be set free.  
_She's not my sister_. Repeated through his head until it became some sort of joke.  
_But I loved her even when I thought she was my sister_. There was no justification for that. It was wrong. He didn't love her like a brother should love a sister. He loved her more.  
_But she is NOT my sister.  
_

He couldn't put his thoughts at ease as there were too many that worried him.  
This journey, he didn't think would change that, but he knew it would do him some good. This was the road less traveled by shadowhunters now that they had the ability to travel without needing to spend precious time walking.

Jace pictured a small book in his head that his father had given him as a child. With a boy called Jonathan Shadowhunter, who gained the mortal instruments before traveling across the land by foot to find a place where he could grow a city of his kind. The story tells about how within the centre of the land, where it was most isolate, a lost civilization can be found, of all different shadowhunters, werewolf's, Vampires and warlocks lived in harmony together. They had a secret source which changed there being into something unimaginable.

"It's a story Jonathan; get your head out of the clouds!" Valentines words echoed through his mind. "You are a fighter!" His bellowing voice even scared Jace now, but then he had thrown his life goals behind of peace and Harmony and began to except his father's view of the world.

**

Concentrate, was all that ran through Clary's head as the footsteps grew closer. They were too heavy to be human, or at least Sebastian's which helped Clary relax a bit as her heart beat so fast that she was begining to feel sick. The heavy clunk of the feet hitting the ground made the floor shake slightly as it grew nearer and nearer.

The fireworks danced across the painting. Creating a whirlpool effect. The sight was spectacular. The colours of the runes drifted slowly to the sides till there was a gap large enough for Clary to fit her up in and with that she pulled out the most spectacular sword. The one the silent brothers had mentioned to her before the uprising of valentine.

Legend had it that many of shadowhunters had tried to replicate the mortal instruments. With the use of magic, demons and runes some created masterpieces which helped them to win any battle with demons. However some turned rather disastrous, putting the sword holder in danger every time it was used. And due to this, experimenting with weapons became impossible under the Clave, and any which were found were taken into possession, and destroyed, but those which could not be, were hidden where no shadowhunter would ever gain their advantage.

Growing closer, the footsteps began to turn into many rather then the one Clary had heard not long ago. The smell of rotting flesh began to grow making Clary aware that she could be about to face an army of forsake. She was too scared to try the sword within the boundaries of the walls, as she was unsure of its effects. Instead she scribbled a portal and leaped through, making sure it closed right behind her as a mist began to hide her views of the rest of the room.

**


	4. Chapter 4

Hey to everyone who was reading my story before, I'm really sorry about it taking THIS long to add a chapter, I have excuses, yes, but I doubt you want to hear them. (It's only short but I have more coming) I re-read my own story and realised it is no story without Jace. Please review and I promise never to take this long ever again

At night central part was empty, due to the fearless rangers, patrolling the area. Clary sat on a park bench to gather her thoughts, the sword laid across her legs.

She imagined the powers it could hold. It was the greatest weapon she could use against her brother. She wasn't a fighter, so she needed some advantage. When she was in Idris the year before, Valentine had had possession of the Mortal instruments. Now they were in the hands of the Clave, she didn't know what had become of them; in their eyes she was a child and had no right to know.

When she had met Jace, He was invisible to everyone in pandemonium. Simon thought she was crazy, and it wasn't long after they had notified security that they did too. She imagined that was how Issi was thinking of her now. No one knew that Sebastian had survived except her, she had known since that night that Valentine died.

Her reasons for not telling anyone were not because she was afraid, but because she felt sorry for him. Jace had been raised a warrior, but was later neglected and sent to live with the lightwoods. She couldn't blame Sebastian for what he was, as it was valentines influence, and with him gone, maybe Sebastian would sort himself out, eventually be able to see his mother, give her the respect she wished he had given her.

Enough, she thought as she considered the many objectives she had to fight him tonight.

It was about Luke now, her almost-step father, another member of the circle.

With the sword in one hand and her stele she edged on into the night. Glorious inked tattoos covered her arms, protecting her, helping her.

She was about halfway across the park when she saw them. The sealie court had uprisen. They were headed towards her, weapons in hand, their faces strong and painful. They had reached her before she had time to react and in a further moment she was surrounded. She held her sword up high in the air as she chanted a song of the angels. If she was going to die tonight, she was going to die trying.

Clary woke in the grass. Her clothes soaked in a soft liquid. The sword laid neatly at her side. Confusion hit her as she wiped her head. What had happened? She held her breath to gain the courage to analyse the situation. It was then that she became aware she wasn't alone.

Reaching for her sword she did what would be considered a ninja move to find her feet. She wobbled slightly before almost toppling back to the ground.

Someone was laughing at her. The laugh familiar, But in the dark she couldn't see the face.

"Show yourself," she panted, only now realising the pain she was in. Her whole body ached, throbbing with every heart beat. Jace walked out of the shadows. Caught off guard Clary jumped, before holding the sword up higher.

"It can't be.. your... here? ...what? how do I know your real?" Her voice was needy, but she knew that demons could replicate humans, maybe this one got smart.

"I thought you may need a hand," his blond hair blew slightly in the cold night. Clary felt goosebumps rise on her skin as felt a surge of energy run through her. But it still didn't seem right.

"Prove it's you," tears fell from her eyes. She had wished for him to come back, she and pictured this moment over and over in her head. She lowered the sword slightly, staring off into the distance. Looking for any detail which showed that the Seelie court had been here, that they had attacked her.

"You look cute when you're scared," A teasing smile made his face seem more like an angels the a demons. She stood there just staring. "On your sixteenth birthday I gave you a witchlight, we were in the garden at the institute. I kissed you, and knew, just knew that I wanted to be with you together."

Clary dropped her sword to the floor before collapsing in pain next to it. In a swift movement, fragile and unearthly Jace was sitting next to her. Staring into her warm, sad eyes.

"How?" she gazed past his moonlight blond hair to the stars above. Everything was such a mess. But she was no longer alone; she had Jace back, that was all she needed.

"The fearies told me they were going to unleash and attack my girlfriend, I came to watch the show," His eyes widened with humour again, before swallowing her sadness. Her pain was his pain.

"Issi called me, she was worried, she said that you thought that Valentines son was alive, that you had lost it." He lent forward closer to her as he breathed softly over her face.

"You don't believe me." She whispered the words which seemed harder to say then think. Jace pulled her head into his lap as he twisted her firey hair through his fingers.

"I trust you with my life." His lips met hers, and for the first time in ages she felt truely happy. She was complete. All the longing and loneliness didn't matter. She forgot her fears of her brother and her pain. Tonight she was Jace's. She was always his.


	5. Chapter 5

Hey guys, the next chap should be up soon after this on, probably gunna be called chapter 6 as i forget how to change the name of chapters please please Review xx

(Mean while... where Luke is)

Ice formed across the glass windows, blocking out the world of Manhattan. On the solid wooden floor lay a man. His body crumpled and curled as thick red liquid ran from his morphing body. His body shivered with cold and fear as he focused on controlling his breathing, if he couldn't do that then he had no chance to survive and warn the others.

With a slight creaking noise the door slid open, only enough for light to filter the room. A small gasping noise echoed as a tall shadow entered the room.

"Lucian," the voice was sour and unfamiliar to his ringing ears. His attacker stood metres away as a defenceless Luke used all his courage to rise. The pain he felt was enthralling, as he lifted to meet the eyes of the man who brought him here.

"You look like your father Johnathan," His voice was a sigh of pain as he struggled to retain his fearless stance.

Sensing his fear and pain, Valentines son places a small bowl on the floor and retreated from the room. He had no use for Lucian if he was not strong, and under the right influence he would obey him. There was only one piece missing in his puzzle, and she didn't even know she was necessary yet.

Jace leaned over Clary's fragile body. She had slept for hours, allowing her body to regain some strength, but he couldn't allow her to sleep any longer. He knew that the Seelie court would never act to harm anyone unless they were in harm themselves, which could only mean Sebastian or Jonathon as he should probably be called. That was his name though, and he felt no need in sharing it with the child of a demon. He was pretty sure Clary felt the same.

Slightly shaking her he began to whisper legends of shadow hunter history. To him they were like nursery rhymes, where the words were always remembered. The tune twinkled with the stars as she woke silently.

"The Seelie court," he stood and pulled her up, allowing her time to straighten her hair and clothes.  
"There is something not right, they wouldn't act out unless provoked."

Clary nodded as she fiddled with the sword in her hands. The night had gotten colder, and she wasn't aware how much time had passed. All she could think of now was Luke, he still could be alive. She had to find him.

It was hours before the door reopened in Luke's room. He had begun to fear the night as he lay shaking in on the cold hard floor. It was too dark to see anything bar the light entering under the door. As far as he could tell, that was the only way out.

Jonathon's slender body slipped through the door. He paced silently to where Luke lay, his glare evident in the pitch black of night.

"Eat!" he ordered, pointing at the bowl he had placed before. Luke didn't move. He did not want to risk what was in the food. He did not want to risk the effects it may have on his body. Jonathon kicked the bowl towards him, close enough for the strong scent of meat and herbs engulfed his body. He felt his inner wolf shake with pleasure as he gallantly turned down the food yet again.

"Then you choose death," His words were harsh. Pulling a witchlight out of his pockets, he examined Luke's body laying on the ground. His mother eyes became visible through the simple glow of the stone. As he pulled a blade out from around his waist and held it directed towards Luke's heart.

As Jace and Clary walked through the night Clary began to remember then night she had found out that Sebastion- Jonathon was her brother. Anger had crossed her face as she imagined the scene where her parents had lived. He had been to sincere, then within a moment he had changed, forcing himself onto her. He escape may have been lucky but as the battle in Idris began it was _him_ who had caused her the most hurt.

Her own brother was willing to harm her.

When she learnt the news of her mother's child who died before she was born she felt sympathetic. Imagining what her life would have been like if she had had a brother to care for her, protecting her from boys and bullies. She envied people with siblings, and now her sibling only envied those with more power than him.

They were so opposite. The demon and the angel swimming through the blood of their parents. The combination striking off contradiction. Something told her that only she had the power to defeat him. But then there was Jace. With the blood of an angel as well. How did he fit into happy families?

He would be harmed. She knew it and she couldn't bear the thought of her brother killing her boyfriend. They were sworn enemies, and relations weren't considered with Sebastian.

But could she find the courage to leave him, even harm him enough to save him from the harmful rathe of her brother?


End file.
